diff isescan.xml @ 0:debe9c750cdd draft

planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isescan.xml	Thu Sep 01 09:29:56 2022 +0000
@@ -0,0 +1,87 @@
+<tool id="isescan" name="ISEScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description> Insertion Sequence Elements detection in prokaryotic genomes </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' input &&
+        isescan.py
+        --seqfile input
+        --output 'results'
+        $remove_short_is
+        --nthread \${GALAXY_SLOTS:-7}
+        #if '$log_activate'
+            | tee '$logfile'
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta" label="Genome fasta input" help="Fasta sequence to analyse for IS"/>
+        <param name="remove_short_is" argument="--removeShortIS" type="boolean" truevalue="--removeShortIS" falsevalue=""
+               label="Remove incomplete IS elements"
+               help="Remove partial IS elements which include IS element with length &gt; 400 or single copy IS element without perfect TIR"/>
+        <param name="log_activate" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Keep the log file"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="logfile" from_work_dir="results">
+            <filter> log_activate == True </filter>
+        </data>
+        <data format="tabular" name="summary" from_work_dir="results/input.sum"/>
+        <data format="tabular" name="all_results" from_work_dir="results/input.tsv"/>
+        <data format="gff" name="annotation" from_work_dir="results/input.gff"/>
+        <data format="fasta" name="is_fasta" from_work_dir="results/input.is.fna"/>
+        <data format="fasta" name="orf_fna" from_work_dir="results/input.orf.fna"/>
+        <data format="fasta" name="orf_faa" from_work_dir="results/input.orf.faa"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="7"> <!-- TEST_1 default parameters -->
+            <param name="input_file" value="NC_012624.fna"/>
+            <output name="logfile" value="TEST_1/test_1.log" lines_diff="70"/>
+            <output name="summary" value="TEST_1/test_1.fna.sum" lines_diff="2"/>
+            <output name="all_results" value="TEST_1/test_1.fna.tsv" lines_diff="1"/>
+            <output name="annotation" value="TEST_1/test_1.fna.gff" lines_diff="1"/>
+            <output name="is_fasta" value="TEST_1/test_1.fna.is.fna" lines_diff="1"/>
+            <output name="orf_fna" value="TEST_1/test_1.fna.orf.fna" lines_diff="1"/>
+            <output name="orf_faa" value="TEST_1/test_1.fna.orf.faa" lines_diff="1"/>
+        </test>
+        <test expect_num_outputs="7"> <!-- TEST_1 remove short is -->
+            <param name="input_file" value="NC_012624.fna"/>
+            <param name="remove_short_is" value="true"/>
+            <output name="logfile" value="test_2.log" lines_diff="50"/>
+            <output name="summary" value="test_2.fna.sum" lines_diff="1"/>
+            <output name="all_results" value="test_2.fna.tsv" lines_diff="1"/>
+            <output name="annotation" value="test_2.fna.gff" lines_diff="1"/>
+            <output name="is_fasta" value="test_2.fna.is.fna" lines_diff="1"/>
+            <output name="orf_fna" value="test_2.fna.orf.fna" lines_diff="1"/>
+            <output name="orf_faa" value="test_2.fna.orf.faa" lines_diff="1"/>
+        </test>
+        <test expect_num_outputs="6"> <!-- TEST_1 remove short is and no logfile -->
+            <param name="input_file" value="NC_012624.fna"/>
+            <param name="remove_short_is" value="true"/>
+            <param name="log_activate" value="False"/>
+            <output name="summary" value="test_2.fna.sum" lines_diff="1"/>
+            <output name="all_results" value="test_2.fna.tsv" lines_diff="1"/>
+            <output name="annotation" value="test_2.fna.gff" lines_diff="1"/>
+            <output name="is_fasta" value="test_2.fna.is.fna" lines_diff="1"/>
+            <output name="orf_fna" value="test_2.fna.orf.fna" lines_diff="1"/>
+            <output name="orf_faa" value="test_2.fna.orf.faa" lines_diff="1"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+      **What it does**
+      ISEScan is a python pipeline to identify Insertion Sequence elements (both complete and incomplete IS elements) in genome.
+      If you want isescan to report only complete IS elements, you need to set command removeShortIS.
+
+      **Input data**
+      ISEScan accept fasta file format as input
+
+      **Parameters**
+      You can remove the short partial IS elements which include IS element with length < 400 or single copy IS element without perfect TIR/>
+
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>